Apple loads every time I restart the computer like it is installing an update-

after updating the OS to yosemite. I had the common Java Runtime Environment Problem "To view this web content, you need to install the Java Runtime Environment.  Click "More info..."to visit the the website for the Java Runtime Environment"  pop up ALL THE TIME-up then installed upgrade to 8.25
then had graphics problem then I did something stopped graphics problem then one of my apps needed java 6 installed java 6 but program still didn't work. Uninstalled program. now have the apple pop up like the computer is installing every time I restart the computer.  it is not instant or near instant start up like it was before.
Suggestions please
I hav
Tried looking for java in application and it is not there
I just typed java -version in Terminal and it came up with the following
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-466.1-11M4716)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-466.1, mixed mode)
Suggestions please
I have late 2013 MBP - retnia 15in 16 gb ram dual graphics 500gb hd
Tried looking for java in application and it is not there

The progress bar is normal on Yosemite. Startup is slower, also.

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